Wednesday, December 31, 2008

microarray versus next generation sequencing

It is the opinion of some life-sciences tool vendors (not my opinion) that digital gene-expression applications performed on second-generation sequencing platforms will replace microarrays as the platform of choice for gene-expression. Let's take a closer look at the reality...

What is important is the knowledge of which genes are altered with regards to expression in response to a specific biological state. Microarrays provide that information on which genes are altered and provide a means of discovering pathway and ontology for sets of genes. This is the most valuable insight into the biology that microarrays provide.

Still others continue to argue that those who are interested in looking at splice variants and alternative transcripts will be the users of digital gene expression using sequencing technology. However, microarrays for alternative splicing are readily available....microarrays to specific transcripts are easily made. No significant advantage for sequencing. Still other researchers studying organisms with limited or no sequence data...will they make the move? They might if sequencing methods are less expensive than creating a cDNA library, making cDNA microarrays and then sequencing the interesting genes they discover. Of course sequencing ESTs is useful in generating a good cDNA library, a nice application for 2nd generation sequencers? However, as much as we do not want to admit it, cost is always an issue....how much does it cost....are always the first words out of a scientists mouth as soon as he sees a tool or technology he or she is interested in.

Another opinion (one that makes sense to me) is that next generation sequencing and microarrays are complimentary technologies. For example, it makes good sense to use microarrays to study a large population of samples, identify representative samples or outliers, and then apply digital gene expression to that smaller number of samples. This approach will provide a more cost effective solution and accurate data.

Data being the key word here, analyzing microarray gene expression data is reaching a maturity with many good software tools readily available both commercially and with open source freeware. The data analysis support for digital gene expression using sequencing is simply not robust at this point.

What is clear is microarray sample preparation is easier and the image analysis is faster and more convenient. Here at Arrayit, we are in a unique position in the market, having focused on an ex-situ universal microarray platform, rather than a second-generation sequencing platform that could support digital gene expression. That makes us a market leader in the ability to provide expression arrays, CGH, SNP as well as all types of protein microarrays. Which means our business will not take a substantial hit should digital gene expression using sequencers gain wider adoption at the expense of microarrays.

Arrayit views next-generation sequencing as a complementary technology that will generate new content which we can analyze on our ex-situ microarray platform. When choosing choosing between sequencing and microarray for gene expression the parameters are simply cost, throughput, and data analysis. That makes microarray the platform of choice.